Introduction

The MEME suite provides online tools for discovering and using protein and DNA sequence motifs. A motif is a pattern of nucleotides or amino acids that appears repeatedly in a group of related DNA or protein sequences. The MEME suite represents motifs as position-dependent scoring matrices.

The MEME suite consists of programs which allow you to:

• meme - for discovery of motifs shared by a group of sequences,
• mast - for search of databases for sequences containing these motifs,
• tomtom - for searching databases of motifs for similar motifs,
• gomo - for finding Gene Ontology terms linked to the motifs,
• glam2 - for discovery of gapped motifs,
• glam2scan - for scanning sequences with gapped motifs,
• fimo - for scanning sequences with motifs,
• mcast - for finding motif clusters,
• meme-chip - for analysis of large DNA datasets like ChIPseq output,
• spamo - for finding motif complexes by analysing motif spacing,
• dreme - for discovery of short regular expression motifs,

and that’s just the web enabled tools.

You can download the C source code for MEME suite from http://meme-suite.org/doc/download.html

You can also use the MEME suite via its website at http://meme-suite.org .

Citing

To cite the full MEME suite, please cite:

Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith,
Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li,
William S. Noble, “MEME SUITE: tools for motif discovery and searching”,
Nucleic Acids Research, 37:W202-W208, 2009.

To cite individual tools, please check the citation page:
http://meme-suite.org/doc/cite.html

Installation

See doc/install.html for operating system requirements, prerequisite software, and installation instructions.

Documentation

Documentation is available online at http://meme-suite.org/doc/overview.html otherwise look in the doc/ folder for overview.html as a place to start.
If you did installation with the --enable-web switch, the html documentation will be installed with the website at <website>/meme_<version>/doc/overview.html.

Problems and comments

Please address any problems or comments to:
meme-suite@uw.edu or
https://groups.google.com/forum/#!forum/meme-suite

Release Notes

See file <distribution-path>/doc/release-notes.html
or after a basic install see <install-path>/doc/release_notes.html
or for a website install see <website>/meme_<version>/doc/release-notes.html

Developers Notes

To prepare a new release.

1. Clone from bitbucket (you have to be granted access to this mercurial repository):

   hg clone ssh://hg@bitbucket.org/tlbailey/meme

2. Create a release branch (Note: the version number is set in configure.ac using variable AM_INIT_AUTOMAKE.):

   hg branch meme_VERSION
   hg ci -m “Create release branch for VERSION”

3. Once you are ready to create a release candidate tag the current revision (this is used to determine the release date and release revision):

   hg tag meme_VERSION_0

   3.1. If you later have to create another release candidate after applying some patches then move the tag so that the release date and release revision are correct:

   hg tag -f meme_VERSION_0

4. Create the example output files by building a copy of the MEME Suite, ensuring it is first in your path, and running create_examples.pl:

   cd meme/doc/examples
   ./create_examples.pl
   scp examples.tgz http://meme-suite.org/meme-software/example-output/examples.tgz # ok so this line doesn’t really work but you should get the intent

5. To create a distribution tar ball meme_VERSION.tar.gz.

   cd meme
   hg purge –all
   ./bootstrap
   ./configure –enable-web –enable-opt –enable-build-libxml2 –enable-build-libxslt
   make dist